From its humble reincarnation, it was as a guerilla army consisting of one Starbase, two ships, and 2,051 Human crew. The spirit of the Alliance had endured 20 years of subjugation as original members were keen to re-enlist, after necessary obstacles were cleared, hitherto uncontacted worlds enlisted and a pair of Battle Thralls were (possibly) persuaded to defect and fight to liberate our corner of the galaxy from Ur-Quan rule.

The Earth Starbase serves as both the command and control centre for the New Alliance as well the support base for the The Flagship and its escort fleet. The crew consists of roughly 2000 Humans, under the leadership of Commander Hayes. When races formally join the Alliance, or seek contact with the Captain, they send delegations to the Starbase.

The Precursor tug constructed at Unzervalt becomes the The Flagship and beacon of hope of the New Alliance. Even with limited modules, it is able to hold it's own in battle and convince vanquished allies to rejoin the fight. It can carry up to ten Planet Landers that are vital to the Alliance for collecting resources and devices while exploring the surfaces of planets.

When it first calls at Earth, its escort fleet consists of just the Tobermoon, the last of the EarthlingCruisers, but the fleet grows in diversity and can include up to twelve ships. Crew members can rotate between ships in the fleet.

There are 13 races who can be persuaded to join the coalition, but how many actually enlist is largely contingent on player actions. Just making contact with the Orz or Zoq-Fot-Pik will be enough for them to join; the same can be said for the Pkunk, but their ships will never be available for construction at the Starbase. To get the Shofixti or Syreen into the fold, the Captain will have to complete several complex objectives. Three other races will trade with the Captain, thus assisting the Alliance.

Up to ten full members send delegations to the Earth Starbase, including captains and ship construction plans, so that their ships can be built for the Flagship's escort fleet. Commander Hayes will typically report this information to the Captain.

1Note that the "New Alliance of Free Stars" is one of the choices of terms in the game for the confederation. Other choices are available: "The Concordance of Alien Nations", "The United Federation of Worlds", and "The Empire of {The Captain}" ("The Captain" is replaced with the captain's name).